Wow

.prettierrc.json

@@ -1,7 +1,7 @@
 {
   "semi": false,
-  "singleQuote": true,
   "trailingComma": "all",
+  "singleQuote": true,
   "arrowParens": "avoid",
   "proseWrap": "always"
 }

src/bai.ts

@@ -26,6 +26,8 @@ function reg2bins(beg: number, end: number) {
 }
 
 export default class BAI extends IndexFile {
+  public setupP?: ReturnType<BAI['_parse']>
+
   async lineCount(refId: number, opts?: BaseOpts) {
     const indexData = await this.parse(opts)
     return indexData.indices[refId]?.stats?.lineCount || 0
@@ -166,10 +168,12 @@ export default class BAI extends IndexFile {
     }
 
     const indexData = await this.parse(opts)
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!indexData) {
       return []
     }
     const ba = indexData.indices[refId]
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!ba) {
       return []
     }
@@ -181,10 +185,11 @@ export default class BAI extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (ba.binIndex[bin]) {
           const binChunks = ba.binIndex[bin]
-          for (const chunk of binChunks) {
-            chunks.push(new Chunk(chunk.minv, chunk.maxv, bin))
+          for (const binChunk of binChunks) {
+            binChunks.push(new Chunk(binChunk.minv, binChunk.maxv, bin))
           }
         }
       }
@@ -199,11 +204,27 @@ export default class BAI extends IndexFile {
     for (let i = minLin; i <= maxLin; ++i) {
       const vp = ba.linearIndex[i]
 
+      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
         lowest = vp
       }
     }
 
     return optimizeChunks(chunks, lowest)
   }
+
+  async parse(opts: BaseOpts = {}) {
+    if (!this.setupP) {
+      this.setupP = this._parse(opts).catch((e: unknown) => {
+        this.setupP = undefined
+        throw e
+      })
+    }
+    return this.setupP
+  }
+
+  async hasRefSeq(seqId: number, opts: BaseOpts = {}) {
+    const header = await this.parse(opts)
+    return !!header.indices[seqId]?.binIndex
+  }
 }

src/indexFile.ts

@@ -1,12 +1,10 @@
 import { GenericFilehandle } from 'generic-filehandle'
-import VirtualOffset from './virtualOffset'
 import Chunk from './chunk'
 import { BaseOpts } from './util'
 
 export default abstract class IndexFile {
   public filehandle: GenericFilehandle
   public renameRefSeq: (s: string) => string
-  public setupP?: Promise<any>
 
   /**
    * @param {filehandle} filehandle
@@ -23,7 +21,6 @@ export default abstract class IndexFile {
     this.renameRefSeq = renameRefSeq
   }
   public abstract lineCount(refId: number): Promise<number>
-  protected abstract _parse(opts?: BaseOpts): Promise<any>
   public abstract indexCov(
     refId: number,
     start?: number,
@@ -36,28 +33,4 @@ export default abstract class IndexFile {
     end: number,
     opts?: BaseOpts,
   ): Promise<Chunk[]>
-
-  _findFirstData(data: any, virtualOffset: VirtualOffset) {
-    const currentFdl = data.firstDataLine
-    if (currentFdl) {
-      data.firstDataLine =
-        currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl
-    } else {
-      data.firstDataLine = virtualOffset
-    }
-  }
-
-  async parse(opts: BaseOpts = {}) {
-    if (!this.setupP) {
-      this.setupP = this._parse(opts).catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-
-  async hasRefSeq(seqId: number, opts: BaseOpts = {}) {
-    return !!(await this.parse(opts)).indices[seqId]?.binIndex
-  }
 }